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## multi2di.R (2022-04-22)
## Collapse or Resolve Multichotomies
## Copyright 2005-2021 Emmanuel Paradis, 2018-2022 Klaus Schliep
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
multi2di <- function(phy, ...) UseMethod("multi2di")
.multi2di_ape <- function(phy, random, equiprob, n)
{
## n: number of tips of phy
degree <- tabulate(phy$edge[, 1])
target <- which(degree > 2)
if (!length(target)) return(phy)
phy <- .reorder_ape(phy, "postorder", FALSE, n, 2L) # by Klaus
pos <- match(target, phy$edge[,1])
nb.edge <- dim(phy$edge)[1]
nextnode <- n + phy$Nnode + 1L
new.edge <- edge2delete <- NULL
wbl <- FALSE
if (!is.null(phy$edge.length)) {
wbl <- TRUE
new.edge.length <- NULL
}
if (random) {
if (equiprob) {
FUN <- function(N) {
x <- rtopology(N, rooted = TRUE)$edge
desc <- x[, 2L]
x[desc <= N, 2L] <- seq_len(N)
x
}
} else {
FUN <- function(N) rtree(N)$edge
}
}
for (i in seq_along(target)) {
node <- target[i]
N <- degree[node]
ind <- pos[i] : (pos[i]+N-1L)
desc <- phy$edge[ind, 2]
if (random) {
## if we shuffle the descendants, we need to eventually
## reorder the corresponding branch lenghts (see below)
## so we store the result of sample()
tmp <- sample(length(desc))
desc <- desc[tmp]
res <- FUN(N)
} else {
res <- matrix(0L, 2*N - 2, 2)
res[, 1] <- N + rep(1:(N - 1), each = 2)
res[, 2] <- N + rep(2:N, each = 2)
res[seq(1, by = 2, length.out = N - 1), 2] <- 1:(N - 1)
res[length(res)] <- N
}
if (wbl) {
## keep the branch lengths coming from `node'
el <- numeric(dim(res)[1]) # initialized with 0's
el[res[, 2] <= N] <-
if (random) phy$edge.length[ind][tmp] else phy$edge.length[ind]
}
## now substitute the nodes in `res'
## `node' stays at the "root" of these new
## edges whereas their "tips" are `desc'
Nodes <- c(node, nextnode:(nextnode + N - 3L))
res[, 1] <- Nodes[res[, 1] - N]
tmp <- res[, 2] > N
res[tmp, 2] <- Nodes[res[tmp, 2] - N]
res[!tmp, 2] <- desc[res[!tmp, 2]]
new.edge <- rbind(new.edge, res)
edge2delete <- c(edge2delete, ind)
if (wbl) new.edge.length <- c(new.edge.length, el)
nextnode <- nextnode + N - 2L
phy$Nnode <- phy$Nnode + N - 2L
}
phy$edge <- rbind(phy$edge[-edge2delete, ], new.edge)
if (wbl)
phy$edge.length <- c(phy$edge.length[-edge2delete], new.edge.length)
if (!is.null(attr(phy, "order"))) attr(phy, "order") <- NULL
if (!is.null(phy$node.label))
phy$node.label <-
c(phy$node.label, rep("", phy$Nnode - length(phy$node.label)))
phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L) # fix by Klaus (2017-01-16)
## the node numbers are not in increasing order in edge[, 2]: this
## will confuse drop.tip and other functions (root), so renumber them
newNb <- integer(phy$Nnode)
newNb[1] <- n + 1L
sndcol <- phy$edge[, 2] > n
## reorder node labels before changing edge:
if (!is.null(phy$node.label)) {
o <- 1 + rank(phy$edge[sndcol, 2])
## the root's label is not changed:
phy$node.label <- phy$node.label[c(1, o)]
}
## executed from right to left, so newNb is modified before phy$edge:
phy$edge[sndcol, 2] <- newNb[phy$edge[sndcol, 2] - n] <-
n + 2:phy$Nnode
phy$edge[, 1] <- newNb[phy$edge[, 1] - n]
phy
}
multi2di.phylo <- function (phy, random = TRUE, equiprob = TRUE, ...)
.multi2di_ape(phy, random, equiprob = equiprob, length(phy$tip.label))
multi2di.multiPhylo <- function(phy, random = TRUE, equiprob = TRUE, ...)
{
labs <- attr(phy, "TipLabel")
oc <- oldClass(phy)
class(phy) <- NULL
if (is.null(labs)) phy <- lapply(phy, multi2di.phylo, random = random, equiprob = equiprob)
else {
phy <- lapply(phy, .multi2di_ape, random = random, equiprob = equiprob, n = length(labs))
attr(phy, "TipLabel") <- labs
}
class(phy) <- oc
phy
}
di2multi <- function(phy, ...) UseMethod("di2multi")
## by Klaus (2018-05-28, 2022-03-24)
.di2multi_ape <- function(phy, tol = 1e-08, ntips, tip2root = FALSE)
{
if (is.null(phy$edge.length)) stop("the tree has no branch length")
phy <- .reorder_ape(phy, "cladewise", FALSE, ntips, 1L) # by Klaus
e1 <- seq_len(max(phy$edge))
ind <- which(phy$edge.length < tol & phy$edge[, 2] > ntips)
n <- length(ind)
if (!n) return(phy)
## new 24.3.22
if (tip2root) {
## nh <- node.depth.edgelength(phy)
phy_tmp <- .reorder_ape(phy, "postorder", FALSE, ntips, 2L)
m <- phy_tmp$Nnode
nh <- .C(node_depth_edgelength, as.integer(phy_tmp$edge[, 1]),
as.integer(phy_tmp$edge[, 2]), as.integer(nrow(phy_tmp$edge)),
as.double(phy_tmp$edge.length), double(ntips + m))[[5]]
}
for (i in ind)
e1[phy$edge[i,2]] <- e1[phy$edge[i,1]]
phy$edge[, 1] <- e1[phy$edge[, 1]]
node2del <- phy$edge[ind, 2]
phy$edge <- phy$edge[-ind, ]
phy$edge.length <- if (tip2root) nh[phy$edge[, 2]] - nh[phy$edge[, 1]] else phy$edge.length[-ind]
phy$Nnode <- phy$Nnode - n
e1 <- sort(unique(phy$edge[, 1]))
tmp <- integer(max(phy$edge))
tmp[e1] <- ntips + seq_len(phy$Nnode)
tmp[1:ntips] <- seq_len(ntips)
phy$edge[] <- tmp[phy$edge]
if (!is.null(phy$node.label))
phy$node.label <- phy$node.label[-(node2del - ntips)]
phy
}
di2multi.phylo <- function (phy, tol = 1e-08, ...)
.di2multi_ape(phy, tol, length(phy$tip.label), ...)
di2multi.multiPhylo <- function(phy, tol = 1e-08, ...)
{
labs <- attr(phy, "TipLabel")
oc <- oldClass(phy)
class(phy) <- NULL
if (is.null(labs)) phy <- lapply(phy, di2multi.phylo, tol = tol, ...)
else {
phy <- lapply(phy, .di2multi_ape, tol = tol, ntips = length(labs), ...)
attr(phy, "TipLabel") <- labs
}
class(phy) <- oc
phy
}
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